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      ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement.

      1 ,
      Nucleic acids research
      Oxford University Press (OUP)

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          Abstract

          Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule. It has been shown recently that half of the known protein movements can be modelled by using at most two low-frequency normal modes. Applications of NMA cover wide areas of structural biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening and closure, potential movements of the ribosome, and viral capsid maturation. Another, newly emerging field of NMA is related to protein structure determination by X-ray crystallography, where normal mode perturbed models are used as templates for diffraction data phasing through molecular replacement (MR). Here we present ElNémo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the 'rotation-translation-block' (RTB) approximation implemented in ElNémo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNémo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors). Any number of normal mode perturbed models for MR can be generated for download. If two conformations of the same (or a homologous) protein are available, ElNémo identifies the normal modes that contribute most to the corresponding protein movement. The web server can be freely accessed at http://igs-server.cnrs-mrs.fr/elnemo/index.html.

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          Author and article information

          Journal
          Nucleic Acids Res
          Nucleic acids research
          Oxford University Press (OUP)
          1362-4962
          0305-1048
          Jul 01 2004
          : 32
          : Web Server issue
          Affiliations
          [1 ] Information Génomique & Structurale (UPR CNRS 2589), 31, chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. karsten.suhre@igs.cnrs-mrs.fr
          Article
          32/suppl_2/W610
          10.1093/nar/gkh368
          441506
          15215461
          7fa07868-c262-49ba-ac9c-81b5e0de03fb
          History

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